title: FC1242_OVA rep 3

type: RNA

city: Verona

first: Francesco

last: De Sanctis

address: Piazzale L.A. Scuro, 10

department: Department of Medicine

country: Italy

institute: University and Hospital Trust of Verona

description: Gene expression data from FC1242 OVA cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: The analysis was performed with the R/Bioconductor platform. The raw probe level signals of the microarray were processed for background correction, normalization and summarization using the robust multichip average algorithm (RMA). Differential gene expression analysis between FC1199-OVA and FC1242-OVA was performed using the limma package.

label: Biotin

source_name: Mouse FC1242 (H-2b) KPC-derived cell line infected with ovalbumin and GFP-encoding lentivirus

label_protocol: Labeling was performed according to Affymetrix One Cycle Target Labeling protocol on HG-U133 Plus 2.0 arrays (Affymetrix, Thermo Fisher Scientific, Waltham, MA, USA)

growth_protocol: Mouse FC1199 (H-2b) and FC1242 (H-2b) were infected for two hours by spin-inoculation 2000 rpm at 20°C and cultured for 48 hours in DMEM 10% FBS with a complete refresh of medium 24 hours after infection

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), and contaminant DNA was removed by RNase-Free DNase Set (Qiagen, Hilden, Germany)

treatment_protocol: Mouse FC1199 (H-2b) and FC1242 (H-2b) KPC-derived cell lines were infected with ovalbumin and GFP encoding lentivirus

value: C57Bl/6 KPC


title: FC1242_OVA rep 2

status: Public on May 14 2024

molecule: total RNA

organism: Mus musculus

tag: strain


title: FC1242_OVA rep 1


title: TMZ-0uM-1₋1

type: SRA

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

library_source: other

data_processing:
The adaptor sequences were trimmed using cutadapt (v1.18) and the untrimmed reads were removed.
sgRNAs were mapped to the annotation file and read count tables were made.
MAGeCK (0.5.8) was used to normalize the count table based on median normalization and fold changes and the significance of the changes in the conditions were calculated for genes and sgRNAs.
Assembly: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: other

organism: Homo sapiens

source_name: brain

growth_protocol: cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
DNA was harvested using DNA isolation kit, and NEB Next® Ultra™ II FS DNA PCR-free Library Prep Kit was used to build database
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: stable sgRNA-expression U251 cells were treated with 200nM or 1500nM TMZ for 72 hours

tag: tissue

value: brain

tag: cell line

tag: cell type

value: tumor


title: FC1199_OVA rep 1

description: Gene expression data from FC1199 OVA cell line

source_name: Mouse FC1199 (H-2b) KPC-derived cell line infected with ovalbumin and GFP-encoding lentivirus


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_4

city: PHILADELPHIA

first: Avital

last: Swisa

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

description:
matrix column name: Control-rep4-P4133
P4133_RNAseq

library_source: transcriptomic

data_processing:
Basecalls performed using NextSeq Control Software 2.2.0.4, RTA 2.4.11 or HiSeq Control Software HD 3.4.0.38, RTA 2.7.7 (for distal colon) and NovaSeq Control Software v1.5 (for proximal)
FASTQ files generated using bcl2fastq v2.20.0.422  (for proximal)
The adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5).
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCm38 mouse transcriptome without bootstraps.
Kallisto count tables were read into edgeR via TxImport, genes with less than 1 cpm across all samples in one group were removed, and differential gene expression analysis was performed between cell types.
Assembly: mm10
Supplementary files format and content: tsv files with normalized abundance (TPM) for each sample generated by Kallisto and csv matrix table with CPM generated with edgeR

molecule: polyA RNA

source_name: proximal colon

extract_protocol:
RNA was extracted from 1 cm segments of colonic tissues using TRIzol reagent (Invitrogen, 15596026) and RNeasy Micro Kit (Qiagen, 74004).
Libraries were made with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530), using the Poly(A) mRNA Magnetic Isolation Module (NEB, E7490)

value: proximal colon

value: Mixed background

tag: group

value: control

tag: genotype

value: Foxa1lox/lox; Foxa2lox/lox

tag: Sex

value: Male

tag: age

value: 11 months


title: embryo25_cell8

city: Edinburgh

first: Lawrence

middle: E

last: Bates

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic single cell

data_processing:
Raw reads were processed as previously (https://doi.org/10.1038/s41467-018-03149-4), aligning to the GRCh38 reference genome using Hisat2 (https://doi.org/10.1038/s41587-019-0201-4).
Gene expression counts were computed from the mapped data using the featureCounts function within RSubread (https://doi.org/10.1093/nar/gkz114).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: Blastocyst

extract_protocol:
Cells were collected directly into 2.5 μl methyltransferase reaction mixture which was comprised of 1 × M.CviPI Reaction buffer, 2 U M.CviPI, 160 μM S-adenosylmethionine, 1 U μl−1 RNAsein, 0.1% IGEPAL then incubated for 15 min at 37 °C. The reaction was stopped and the RNA preserved with the addition of 5 μl RLT plus.
Single-cell RNA sequencing libraries were prepared according to the RNA half of the scNMT-seq protocol (https://doi.org/10.1038/s41467-018-03149-4). Briefly, biotinylated oligo-dT was bound to magnetic beads which were added to single-cell lysates in 96w plates. The captured mRNA was then reverse transcribed and PCR amplified on beads accordingto the Smartseq2 protocol (https://doi.org/10.1038/nprot.2016.138,https://doi.org/10.1038/nprot.2014.006). Indexed Illumina libraries were prepared from the amplified cDNA using Nextera XT reagents and then pooled and sequenced on a HiSeq 2000 instrument using 75bp paired-end reads.

value: Blastocyst

value: ICM

value: WT

tag: developmental stage


title: FC1199_OVA rep 3


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_3

description:
matrix column name: Control-rep3-P3942
P3942_RNAseq

value: 10.5 months


title: embryo25_cell7


title: embryo25_cell6


title: embryo25_cell5


title: PC3OE2

city: Wuhan

first: An

last: Zhang

state: Hubei

address: No.1095 Jie Fang Avenue, Hankou, Wuhan 430030, P.R. China.

institute: Tngji Hospital

data_processing:
Raw RNA-seq reads were aligned to the Ensembl mouse reference genome GRCh38 (hg38) using HISAT2. Gene expression was subsequently quantified using featureCounts. The raw gene counts were processed with the DESeq2 package in R to analyze differentially expressed genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited txt files include FPKM values for each sample

source_name: prostate

extract_protocol:
RNA was extracted using the HiPure Universal RNA Mini Kit (Magen Biotechnology).
RNA libraries for RNA-seq were prepared with VAHTS Universal V6 RNA-seq Library Prep Kit following manufacture's protocols

value: prostate

value: prostate cancer cell

tag: treatment

value: miR-5100 mimic transfection


title: embryo25_cell4


title: embryo25_cell12


title: PC3OE3


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_2

description:
matrix column name: Control-rep2-P3853
P3853_RNAseq

value: 9 months


title: embryo25_cell3


title: embryo25_cell9


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_1

description:
matrix column name: Control-rep1-P3841
P3841_RNAseq

value: Villin1-Cre; Foxa1lox/wt; Foxa2lox/wt


title: embryo25_cell2


title: embryo24_cell12


title: embryo25_cell1


title: PC3NC3

value: miR-NC trasfection


title: embryo24_cell11


title: embryo24_cell10


title: IgG_rep1

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

description: IgG

library_source: genomic

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against mm10 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.6.3) (PMID: 22217937).
Differentially expressed peaks were identified after DESeq2 normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: mm10
Supplementary files format and content: BigWig Track Format of each CUT&Tag sample.
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: primary CD8 T cell

growth_protocol: CD8+ T cells were enriched from the spleens and peripheral lymph nodes of donor mice using a naïve CD8+ T cell isolation kit. Cells were resuspended at 106 per ml in RPMI1640 complete medium with 10% FBS (Gibco), 50 M β-mercaptoethanol, 100 U ml-1 penicillin-streptomycin, non-essential amino acids (Gibco) and sodium pyruvate (Gibco).

extract_protocol:
1 × 10^5  CD8+ T cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Cells were incubated with 1 mg of respective targeting antibodies at 4 °C overnight. 0.5 mg secondary antibody was added and incubated for 1 h at 25 °C. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 14 cycles. Final product was cleaned by VAHTS DNA Clean Beads at a 2 × ratio. Libraries were sequenced on a Novaseq 6000 in a 150 bp/150 bp Paired end run. An average of 20 × 106 paired reads was generated per sample.

treatment_protocol: After 24 hours of activation by anti-CD3/CD28, activated CD8+ T cells were treatment with DMSO or Yoda1 (10 M) for another 24h.

value: primary CD8 T cell

value: DMSO

tag: cut-tag antibody

value: Normal Rabbit IgG(Cell Signaling Technology, 2729)


title: PC3NC2


title: scRNA-seq_αLP_hashtag_v2

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description: TAS-seq

data_processing:
After adaptor removal by Cutadpat, gene-expression libraries were aligned to the mm10 reference transcriptome by Bowtie2, and count matrices were generated using modified BD Rhapsody workflow. Valid cell barcodes were identified as cell barcodes above the inflection threshold of the knee-plot of total read counts of each cell barcode identified by the DropletUtils package. Sample origins and doublets were identified based on fold change of the normalized read counts of the hashtags. The count matrices were imported and analyzed using Seurat v.4.
Assembly: GRCm38
Supplementary files format and content: count matrix

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were harvested from the cut-off of both ends of the femur, tibia and pelvis, humerus, and scapula of mice using a centrifuge. Lineage-positive cells were depleted using a MOJO Hematopoietic Isolation Kit. αLP were sorted using FACSAriaII (v1) and BD Melody (v2).
Hashtag laveled sorted cells were combined, trapped, and reverse-transcribed using BD Rhapsody (BD) according to the manufacturer's instructions. Single-cell RNA sequencing was performed using the platform of TAS-Seq.

value: Bone Marrow

value: WT and G3SEKO

tag: library type

value: hashtag

tag: antibodies/tags

value: Anti-MHC classI,  WT:TotalSeq-A0302, A0303)


title: embryo24_cell9

value: Blastocyst

value: Male


title: FC1199_OVA rep 2

value: C57Bl/6 KPC


title: P300_YODA1_rep2

value: WT

value: anti-p300 (abcam, ab10483)


title: embryo24_cell7

value: ICM


title: scRNA-seq_αLP_mRNA_v2 paired

description: TAS-seq

value: mRNA


title: A-T to G-C base editing efficiency with AC10 circular gRNA at VEGFA gene site in HEK295T cell line

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

data_processing:
Sample indexes were removed by trim_galore(0.6.10).
BAM files were generated by alignment to the reference genomic regions using the Bowtie2(2.5.1).
The substitution at each base was calculated with CRISPResso(2.2.12).
Assembly: hg38
Supplementary files format and content: Quantification of A to G substitution at each target position.

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested by addition of lysis buffer with proteinase K, 55℃ overnight. And then the genomic DNA was extracted with the steps of ethanol precipitation.
The targeted genome regions of interest were amplified with the first round PCR by Gold Medal Mix to add unique indexes for each sample. Each sample was then amplified by the second round PCR using P5 and P7 primers. All PCR products were mixed into one pot and purified by DNA Clean Beads.

treatment_protocol: In 24-well plates, HEK293T cells were transfected with 16ng gRNA plasmids and 484ng dCas12f-ABE or Cas12f-ABE plasmids.

value: Human embryonic Kidney


title: embryo24_cell8


title: embryo24_cell6


title: embryo24_cell5


title: P300_YODA1_rep1


title: PC3OE1

value: prostate

value: prostate cancer cell

value: miR-5100 mimic transfection


title: embryo24_cell4


title: embryo24_cell3


title: A-T to G-C base editing efficiency with AC10 circular gRNA at GS1 gene site in HEK293T cell line


title: beige_Input

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
Reads were filtered with fastp, aligned to the genome with bowtie2, and deduplicated.
Log ratio sample/input tracks were generated using deeptools bwCompare from RPGC normalized tracks created with bamCoverage.
Peaks were called from aligned reads using macs2 with default parameters for H3K4me3 and H3K27ac or with the --broad option for H3K27me3 and H3K4me1.
Assembly: hg38
Supplementary files format and content: Coverage tracks of log ratio sample/input (.grep.norm.bw). Raw coverage tracks for input samples are also provided (.bw).
Supplementary files format and content: Peaks called with macs2.

source_name: primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were isolated from subcutaneous liposuction material. Cells were expanded in DMEM/F12 containing 10% fetal calf serum, and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-8 were used in three independent differentiations into the adipocyte lineage.

extract_protocol:
Day 15 differentiated white and beige samples were trypsinized, resuspended in HBSS, 0,5% BSA, and centrifuged 200g for 5 min to isolate floating mature adipocytes. Purified nuclei were fixed with 1 % formaldehyde; lysed for 10 min in ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, proteinase inhibitors, 1 mM PMSF, 20 mM Na Butyrate) and sonicated for 30 sec ON/OFF for 10 min in a Bioruptor®Pico (Diagenode) into ~200 base-pair fragments. After sedimentation, the supernatant was diluted 10 times and chromatin incubated with anti-H3K27ac (Diagenode c15410174), anti-H3K4me3 (Diagenode c15410003), anti-H3K27me3 (Diagenode c15410069), or anti-H3K4me1 (Diagenode c15410037) antibodies, each at 2.5 μg/106 cells, for 2 h at 4°C. ChIP samples were washed, cross-links reversed, and DNA eluted for 2 h at 68°C. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O.
Libraries were prepared using a Microplex kit (Diagenode) and sequenced on a Nextseq 500 or Novaseq (Illumina).

treatment_protocol: For adipogenic differentiation, confluent cells were cultivated for 72h in DMEM/F12/10% fetal bovine serum without growth factors. For white adipose differentiation ASCs were induced by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was renewed every 3 days until day 9. Cells were then maintained in DMEM/F12/10% fetal bovine serum and 10 µg/ml insulin until day 15. For beige adipose differentiation, media were supplemented with 1 µM rosiglitazone until day 15.

value: primary adipose stem cells

tag: subject

tag: time

value: beige adipogenic differentiation

tag: chip antibody


title: embryo23_cell13

value: Female


title: P300_DMSO_rep2

value: primary CD8 T cell

value: DMSO


title: embryo24_cell2


title: P300_DMSO_rep1


title: embryo24_cell1


title: embryo23_cell10


title: white_Input

value: white adipogenic differentiation


title: embryo23_cell12

value: Blastocyst


title: CREB_YODA1_rep2

value: anti-CREB1 (proteintech, 12208-1-AP)


title: PC3NC1

value: miR-NC trasfection


title: embryo23_cell9

value: WT


title: embryo23_cell8


title: white_H3K4me1_ChIP


title: white_H3K27ac_ChIP


title: beige_H3K4me1_ChIP


title: CREB_DMSO_rep2


title: CREB_YODA1_rep1


title: beige_H3K27ac_ChIP


title: beige_H3K27me3_ChIP


title: embryo23_cell5


title: CREB_DMSO_rep1


title: embryo23_cell4


title: embryo22_cell9

description: lane1_Ferdinand_Embryos_Plate6_H06_CAATTGTT

value: Male


title: RNA_Osr2-KO_rep1

data_processing:
Basecalls were performed using CASAVA version 1.8
All following steps were performed using the CellRanger analysis pipeline (v.7.0.1).
Sample demultiplexing, barcode processing
alignment, filtering
UMI counting and aggregation of sequencing runs
Assembly: mm10
Supplementary files format and content: H5 file containing raw features, barcodes, and matrices (raw_feature_bc_matrix) for each library.

source_name: subcutaneous MC38-OVA tumor

growth_protocol: CD8+ T cells were enriched from the spleens and peripheral lymph nodes of donor mice using a naïve CD8+ T cell isolation kit.

extract_protocol:
Two weeks after adoptive transfer, WT (Osr2fl/fl OT-I CD45.1-CD45.2+) and Osr2 knockout (Osr2fl/fl Lck-Cre OT-I CD45.1+CD45.2+) T cells were flow-sorted for 10X single cell 3' V3 library preparation.
Cells were counted and loaded onto the Chromium Controller (10 × Genomics) for a target recovery of 1 × 10^4 single cells. Samples were processed per the manufacturer’s protocol and sequenced on an Illumina NovaSeq6000 sequencer using a 150-bp kit with paired-end reads.

treatment_protocol: For subcutaneous tumor models, MC38-OVA (1 × 10^6) tumor cells were injected subcutaneously into the flanks of WT recipient mice (CD45.1+). Tumor-engrafted recipient mice were first intraperitoneally injected with 200 mg kg-1 cyclophosphamide (CTX, Aladdin) when the tumor is palpable, then OT-I naive T (1x10^6) cells were adoptively transferred by tail-vein injection into recipient mice.

value: subcutaneous MC38-OVA tumor

value: Osr2fl/fl Lck-Cre OT-I CD45.1+CD45.2+

value: MC38-OVA bearing


title: white_H3K27me3_ChIP


title: RNA_Osr2-KO_rep2


title: embryo23_cell3

value: ICM


title: embryo23_cell2


title: RNA_WT_rep2

value: Osr2fl/fl OT-I CD45.1-CD45.2+


title: embryo22_cell8

description: lane1_Ferdinand_Embryos_Plate6_H05_ATCCCCTA


title: embryo23_cell1


title: embryo23_cell7


title: RNA_WT_rep1


title: embryo23_cell11


title: beige_H3K4me3_ChIP


title: embryo22_cell7

description: lane1_Ferdinand_Embryos_Plate6_G06_GGAATTTC


title: embryo22_cell6

description: lane1_Ferdinand_Embryos_Plate6_F06_GTTTTTCG


title: embryo23_cell6


title: white_H3K4me3_ChIP


title: embryo22_cell5

description: lane1_Ferdinand_Embryos_Plate6_E06_TTGAGCGA


title: embryo22_cell4

description: lane1_Ferdinand_Embryos_Plate6_D06_AGGTCACG


title: embryo22_cell3

description: lane1_Ferdinand_Embryos_Plate6_C06_GAGTGCGA


title: 55002, mouse, hippocampus, 10Wk, control

city: Groningen

first: Bente

middle: Marianne

last: Hofstra

address: Antonius Deusinglaan 1, Building 3211; PO Box 30001, CB50

department: Genetics

country: Netherlands

institute: University medical center Groningen

data_processing:
reads were trimmed for adaptor sequences using the standard parameters in STAR (v2.7.3a-foss-2018b) (sjdbOverhang 100)
Reads were aligned to reference genome GRCm38.102 using STAR (v2.7.3a-foss-2018b)
Readcounts were generated using the FeatureCounts package in RStudio (v1.3.1093)
Assembly: GRCm38.102
Supplementary files format and content: tab delimited txt file including raw counts for each sample

source_name: hippocampus

growth_protocol: Animals were given water and food ad lib on a 12:12 light dark cycle with lights off at 13:00.

extract_protocol:
Animals were decapitated without prior aenestesia and hippocampi were dissected and snap frozen in liquid nitrogen. RNA was extracted using Trizol following manufacturers protocol
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L).

treatment_protocol: Maternal separation was conducted between PND 10-17 for 4 hours per day, alternating in the light (8:00-12:00) and dark cycle (14:00-18:00)

value: hippocampus

value: male

value: wild type

value: control


title: subject6_white_rep2

description:
23-21427_S10
Reanalysis of GSM7109068

data_processing:
Reads were filtered and remaining adaptor sequences trimmed with fastp 0.20.1.
For gene-level analysis reads were aligned to the hg38 genome (GENCODE 32 annotation) with hisat2 (v2.1.0), and counted using featureCounts (v2.0.1). Low abundance genes were filtered using filterByExpr from edgeR and then normalized using the trimmed mean of M values method. Beige and white gene expression was compared pairwise for each donor using the robust eBayes method with limma-voom adjustment.
Genome tracks of Bins Per Million (BPM) mapped reads were generated from hisat alignments with deeptools bamCompare at a binsize of 1 bp for each strand separately.  Then differentiation replicates were averaged with BigwigAverage.
For exon-exon junction analysis reads were aligned to hg38 genome with STAR v2.7.10b using GENCODE 32 reference annotation (ENCODE options from the STAR manual were used as well as --outSAMstrandField intronMotif --outSAMtype BAM Unsorted). Split reads with at least a 6 bp of anchor sequence and an intron length between 20 bp and 1 Mb were extracted using regtools. Introns sharing splice sites were clustered using LeafCutter’s leafcutter_cluster_regtools.py script, requiring at least 30 reads per library supporting each cluster for introns of up to 1 Mb in size.
Differences in intron excision were tested between white and beige triplicates with donor as a confounding variable. Strict prefiltering required that an intron was found in at least 14 (of 36) libraries and that clusters had at least 12 libraries per condition with 20 or more spliced reads. The differential_splicing function from LeafCutter R package v0.2.9 was used to implement the Dirichlet-multinomial generalized linear model (15). LeafCutter assigns a ∆PSI to each intron and a p-value to each cluster, which contains introns that share splice sites and thus belong to alternative isoforms of that gene or genes. Effect size and cluster significance output files were merged to make ∆PSI and cluster p-value information available in one table. Introns were assigned to transcripts, with the priority for annotations: GENCODE 32 > RefSeq  GCF_000001405.40-RS_2023_10 > FANTOM CAT robust (Hon et al. 2017). In other words, only if an intron was missing from the GENCODE annotation was it compared to the RefSeq annotation and so on.
Normalized TRIFID prediction scores were downloaded for the GENCODE 37 and RefSeq110 annotations. Where multiple transcripts were possible for a single intron excision event, TRIFID scores were averaged, but if no score was found -0.1 was used. To calculate a TRIFID difference, the top two intron-excision events were compared for clusters with at least one significant junction (| ∆PSI | > 0.1 & p.adjust < 0.05).
Assembly: hg38 GENCODE 32
Supplementary files format and content: .fwd.bw Bins Per Million (BPM) mapped reads averaged across three differentiation replicates. Read pairs mapped to the forward strand only. Binsize 1bp.
Supplementary files format and content: .rev.bw Bins Per Million (BPM) mapped reads averaged across three differentiation replicates.  Read pairs mapped to the reverse strand only. Binsize 1bp.
Supplementary files format and content: Counts of reads in genes from gencode 32 annotation.
Supplementary files format and content: Fragments per kilobase per million (FPKM) for each gene passing the filtering threshold in each sample.
Supplementary files format and content: perind_numers.junction.counts.gz - Counts of reads spanning each exon-exon junction.
Supplementary files format and content: Information from leafcutter on each exon-exon junction (e.g. cluster id, deltaPSI and  adjusted pvalue), and annotation with reference databases and intron numbers.

extract_protocol:
Total mRNA was isolated from cells using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing.
PolyA-selected RNA was sequenced from paired-end libraries using TruSeq Stranded mRNA kit from Illumina.

treatment_protocol: For adipogenic differentiation, confluent cells were cultivated for 72h in DMEM/F12/10% fetal bovine serum without growth factors. For white adipose differentiation ASCs were induced by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was renewed every 3 days until day 9. Cells were then maintained in DMEM/F12/10% fetal bovine serum and 10 µg/ml insulin until day 15. For beige adipose differentiation, media were supplemented with 1 µM rosiglitazone until day 15. RNA from the total cell population was harvested by direct lysis in the well.

value: primary adipose stem cells


title: embryo22_cell1

description: lane1_Ferdinand_Embryos_Plate6_A06_GGCTACAG


title: embryo22_cell2

description: lane1_Ferdinand_Embryos_Plate6_B06_TAGAACAC


title: 57001, mouse, hippocampus, 10Wk, maternal separation PND10-17

value: Maternal separation


title: subject6_white_rep1

description:
22-21426_S3
Reanalysis of GSM7109067

value: white adipogenic differentiation


title: 57000, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: embryo21_cell13

description: lane1_Ferdinand_Embryos_Plate6_G05_AGGATCTC

value: Blastocyst


title: DC2.4 cells mLCAP-4

city: Hubei

first: 文

last: 李

address: Wuhan

institute: Wuhan University

data_processing:
Different libraries are assembled according to the amount of target data and sequenced on the Illumina platform
Trimmomatic (Version: 0.36; Parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:18 MINLEN:36) was used to clean raw data, and clean data was obtained after data cleaning. HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) (version: 2.2.1) was used for clean reads alignment. After reads alignment, String Tie was used to quantify the above reads.
Supplementary files format and content: Excel file with FPKM, TPM, readcounts for every gene and every sample

source_name: DC2.4 cells

extract_protocol:
mRNA was enriched from total RNA using oligomer (dT) magnetic beads. The mRNA fragments were cut into short fragments of about 300bp using a cleavage buffer. The first cDNA was synthesized by using mRNA as template and random hexamer as primer.
The purified double-stranded cDNA was subjected to terminal repair, A-tail modification and sequencing joint connection. Select fragment size using AMPure XP beads. PCR amplification was performed to obtain the final cDNA library.
Q-PCR and other methods were used for quality control and quantification of the library to ensure that the effective concentration of the library was greater than 2nM

value: DC2.4 cells

value: co-cultured with mLCAP


title: DC2.4 cells mLCAP-2

value: WT


title: 56999, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: subject6_white_rep3

description:
24-21428_S17
Reanalysis of GSM7109069


title: DC2.4 cells mLCAP-3


title: subject4_white_rep1

description:
19-21423_S40
Reanalysis of GSM7109064


title: 54971, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: embryo21_cell12

description: lane1_Ferdinand_Embryos_Plate6_G04_AAGCCTTC

value: Male


title: DC2.4 cells mLCAP-1


title: DC2.4 cells Blank-4


title: 57139, mouse, hippocampus, 10Wk, control


title: embryo21_cell11

description: lane1_Ferdinand_Embryos_Plate6_F05_AACGGCTT


title: subject4_white_rep2

description:
20-21424_S47
Reanalysis of GSM7109065


title: subject5_beige_rep3

value: beige adipogenic differentiation


title: embryo21_cell10

description: lane1_Ferdinand_Embryos_Plate6_F04_TCTACAGT


title: 54972, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: DC2.4 cells Blank-3


title: embryo21_cell9

description: lane1_Ferdinand_Embryos_Plate6_E05_TGTCGACT


title: 55068, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: embryo21_cell14

description: lane1_Ferdinand_Embryos_Plate6_H04_CCATAGCT


title: DC2.4 cells Blank-2


title: embryo21_cell8

description: lane1_Ferdinand_Embryos_Plate6_E04_TTTGGGCA


title: subject6_beige_rep3


title: subject4_white_rep3

description:
21-21425_S54
Reanalysis of GSM7109066


title: 55067, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: DC2.4 cells Blank-1


title: subject1_beige_rep3


title: embryo21_cell7

description: lane1_Ferdinand_Embryos_Plate6_D05_ATCCTAGG


title: 55066, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: embryo21_cell6

description: lane1_Ferdinand_Embryos_Plate6_D04_AGACCGTG


title: subject1_white_rep3


title: subject5_white_rep3


title: 55001, mouse, hippocampus, 10Wk, control

value: Control


title: subject2_white_rep3


title: 54970, mouse, hippocampus, 10Wk, maternal separation PND10-17


title: RC77N/E untreated Rep 2

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

data_processing:
Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle. Real-time analysis (RTA) 2.2.38 software was used to process the image analysis.
Quality of the raw RNAseq read data was assessed using FastQC (v0.11.7)
Read trimming and adapter removal was performed using Trimmomatic (v0.36)
Trimmed reads were aligned to the reference genome (GrCh37) using HISAT2 (v2.1.0)
Gene expression was quantified from alignments using Stringtie (v1.3) and reported in transcripts per million (TPM)
Assembly: GrCh37
Supplementary files format and content: tab-delimited text matrix include TPM values for each Sample

growth_protocol: RC-77N/E was grown in a humidified incubator with 5% CO2 at 37 °C. In accordance with recent guidelines by the National Institutes of Health (NIH) on the authentication of key biological resources, cells were authenticated utilizing Short Tandem Repeat (STR) profiling against the American Type Culture Collection (ATCC) STR database (ATCC, Cat: ATCC 135-XV). RC-77N/E cells were routinely tested for mycoplasma contamination using MycoProbe Mycoplasma Detection Kit (R&D Systems, Minneapolis, U.S.A., Cat: CUL001B). RC-77N/E cell line was provided by C.A. Casiano’s laboratory with permission from J.S. Rhim. RC-77N/E was grown in collagen-coated treated culture dishes in keratinocyte serum-free medium (K-SFM) supplemented with bovine pituitary extract and recombinant epidermal growth factor (Gibco, Grand Island, U.S.A., Cat:17-005-042) and was used for growing and maintaining the cells. Normocin 0.2% (Invivogen, San Diego, U.S.A., Cat: ANT-NR-1) was added to the medium for all cell lines to prevent contamination by mycoplasma, bacteria, or fungi.

extract_protocol:
Before handling RNA, surfaces and instruments underwent treatment with RNase Zap (Ambion AM9780, Austin, U.S.A.). RNA extraction from cultured cells followed the Rneasy Mini protocol (Qiagen 7414, Hilden, Germany). Initially, cells were rinsed with PBS, then lysed with buffer RLT and 10 μL/mL β-mercaptoethanol, utilizing 350 μL per T25 flask or 600 μL per 10 cm plate. Subsequently, the Rneasy Mini protocol, inclusive of on-column incubation with Rnase-free Dnase (Qiagen, Cat: 79254), was adhered to. Post washes, RNA was eluted using 30 μL Rnase-free water, and its concentration was determined employing a Nanodrop spectrophotometer. RNA samples were stored at −80 °C, with each sample being isolated and utilized individually in triplicate.
RNA sequencing was performed by the City of Hope Integrative Genomics Core facility using RNA sequencing libraries prepared with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems, Wilmington, U.S.A., Cat KR1352) according to the manufacturer’s protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51 cycles. Real-time analysis (RTA) 2.2.38 software was used to process the image analysis.

treatment_protocol: For treatment, 1,25-dihydroxyvitamin D3 [1α,25(OH)2D3] (Tocris Bioscience, Bristol, U.K., & Cat: 25-515-0U) reconstituted in 100% ethanol was used. Cells were then treated with 10 nM (physiological concentration) for 24 h[M1][JJ2]. Vehicle (ethanol) was included for every untreated control. The final ethanol percentage for treated and untreated (vehicle control) cell lines was 0.01%.

value: non malignant prostate cell line

value: untreated control


title: subject2_beige_rep3


title: embryo21_cell5

description: lane1_Ferdinand_Embryos_Plate6_C05_GGAGTCTA

value: ICM


title: RC77N/E 10nM 1a25(OH)2D3 treated Rep 2

value: 10nM 1a,25(OH)2D3 treated

value: 24 hours


title: embryo21_cell4

description: lane1_Ferdinand_Embryos_Plate6_C04_GACACTTA


title: 57138, mouse, hippocampus, 10Wk, control

value: hippocampus

value: male

value: wild type


title: RC77N/E 10nM 1a25(OH)2D3 treated Rep 1


title: RC77N/E untreated Rep 3


title: subject4_beige_rep3

value: primary adipose stem cells


title: 55000, mouse, hippocampus, 10Wk, control


title: RC77N/E untreated Rep 1


title: subject3_beige_rep3


title: embryo21_cell2

description: lane1_Ferdinand_Embryos_Plate6_B04_TTCGCACC


title: embryo21_cell3

description: lane1_Ferdinand_Embryos_Plate6_B05_TCTACGAC


title: 54952, mouse, hippocampus, 10Wk, control


title: subject3_white_rep3

value: white adipogenic differentiation


title: 54951, mouse, hippocampus, 10Wk, control


title: human pancreatic islets_3

city: Lausanne

first: Cecile

last: Jacovetti

address: Rue du Bugnon 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing quality was examined by FastQC software and trimmed reads were aligned to mouse and rat mature-tRNA and pre-tRNA sequences from GRCh37/hg19 genome.
For small RNA sequencing, the sequencing type was 50-bp single-read at 145 M reads.
Unique sequences (considering UMI codes) were counted.
We set the minimum cpm value as at least 5 reads in the smallest library. Only sequences above the minimum cpm value in at least 3 samples were retained.
The remaining reads were aligned to the transcriptome sequences (miRNA, piRNA, rRNA, snRNA, snoRNA).
Assembly: GRCh37/hg19 genome
Supplementary files format and content: tab-delimited text file includes raw counts (reads) for each sample.
Supplementary files format and content: tab-delimited text file includes transcript per million 1 (TPM1: read counts normalized by the total deduplicate mapped reads) and TPM2 (read counts normalized by the total deduplicate mapped tRNA reads) values for each sample.
Supplementary files format and content: tab-delimited text file includes tRF sequences, tRF types, host tRNAs and length, numbers of tRNAs from which the tRFs could originate from, anticodon position  for each sample.

source_name: pancreatic islets

growth_protocol: Islets were isolated by enzymatic digestion and density-gradient purification [DOI: 10.1016/j.celrep.2020.108466] and sent in M199 medium (5.5 mmol/L of glucose) to Lausanne, Switzerland where they were dispersed using trypsin/EDTA [DOI: http://dx.doi.org/10.7554/eLife.06990.001]. Human islets cells were then cultured in Connaught’s Medical Research Laboratories (CMRL) 1066 medium supplemented with 10 % fetal calf serum, 100 U/mL penicillin, and 100 μg/mL streptomycin, 2 mM L-glutamine, and 10 mM HEPES. The percentage of β-cells in the human islet preparations was 55.6 ± 15.1 %, determined by insulin immunofluorescence [DOI: 10.2337/db09-1177].

extract_protocol:
Total RNA from human islets was extracted using miRNeasy mini kit (Qiagen # 217004).
Nucleotide modifications were removed from RNA samples prior to sequencing library construction by the following treatments using the rtStar™ tRF&tiRNA Pretreatment kit (Arraystar # AS-FS-005): 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’ adaptor ligation, and N1-methyladenosine (m1A), 3-methylcytidine (m3C) and 1-methyl guanosine (m1G) demethylation. 10 ng of total RNA was used for the construction of sequencing cDNA libraries using QIAseq miRNA NGS 48 Index IL kit (Qiagen # 331595) following manufacturers's protocol.

value: pancreatic islets

tag: gender

value: F

tag: bmi [kg/m2]

tag: disease state

value: healthy


title: embryo21_cell1

description: lane1_Ferdinand_Embryos_Plate6_A05_GATCAGCG

tag: tissue

value: Blastocyst

value: WT


title: human pancreatic islets_2


title: subject5_beige_rep2

tag: cell type

value: beige adipogenic differentiation


title: 57137, mouse, hippocampus, 10Wk, control

tag: strain

value: Control


title: embryo20_cell7

description: lane1_Ferdinand_Embryos_Plate6_H03_TTACACTA

tag: genotype

value: Female


title: human pancreatic islets_1


title: subject5_white_rep2


title: embryo20_cell6

description: lane1_Ferdinand_Embryos_Plate6_G03_TATTCTGG

tag: Sex


title: 55064, mouse, hippocampus, 10Wk, control


title: subject6_beige_rep2


title: 55063, mouse, hippocampus, 10Wk, control


title: 55062, mouse, hippocampus, 10Wk, control


title: embryo20_cell4

description: lane1_Ferdinand_Embryos_Plate6_E03_ATAGCTCT


title: embryo20_cell3

description: lane1_Ferdinand_Embryos_Plate6_D03_ACGTTCAT


title: subject1_beige_rep2


title: Input library (untreated)

city: Nashville

first: Eric

middle: P

last: Skaar

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
Following sequencing, raw files were uploaded to the Galaxy Server from Tufts University to trim the reads, filter for quality, map to the S. aureus genome, and determine fitness using a “Dval” value for every gene in each library pool. A “Dval” score represents the aggregate number of reads for all transposon insertions within a gene in a given library sample, divided by the total number of predicted reads for that gene based on its size and the total number of reads obtained on the library pool. Dval scores in calprotectin treatments were normalized to Dval scores in vehicle control to calculate a fitness score for each gene in each experimental condition. Fitness scores were Log2 transformed and used to calculate a Z-score using the average and standard deviation of the population. A Z-score cutoff for significance was set at two standard deviations away from the mean.
Assembly: Staphylococcus aureus genome (NC_009641)
Supplementary files format and content: File is in .xlsx format. Contains raw sequencing reads as well as normalized abundance (Dval) values and fitness analysis

organism: Staphylococcus aureus

source_name: Bacterial cell

growth_protocol: A single aliquot of frozen S. aureus Newman Transposon library was inoculated 1:50 in 5 mL of TSB and grown for 1 hour at 37°C with shaking at 180 rpm. An aliquot of this input library was also saved for sequencing. After 1 hour of growth, the library was subcultured 1:100 into 5.5 mL aliquots of three different treatment conditions. At 6 hours, cultures were pelleted and stored at -80°C. This experiment was performed in triplicate.

extract_protocol:
genomic DNA (gDNA) from S. aureus cultures was extracted using the DNeasy Blood and Tissue Kit (QIAGEN). All DNA samples were then normalized to 100 ng/mL in ultra-pure water. Samples were then processed using the DTR gel filtration cartridges (Edge Biosystems Inc 42453) using the manufacturer’s recommendations.
The sample (50 mL) was sheared in Covaris tubes using the Covaris LE220 instrument to generate 350bp fragments. Sheared DNA was treated with terminal deoxytransferase to generate a 3’ poly C-tail sequence, and two rounds of nested PCR were employed to amplify transposon junction regions. These products were multiplexed using 8-bp indexing primers and sequenced on the Illumina Hi-Seq 2500 at Tufts University Core Facility.
Transposon sequencing

treatment_protocol: The three different treatment conditions included: vehicle control (60:40 calprotectin buffer to TSB ratio), 300 µg/mL of WTCP, or 600 µg/mL of ∆s1CP.

value: Newman

value: Bacterial cell

value: Transposon library before treatment


title: embryo20_cell2

description: lane1_Ferdinand_Embryos_Plate6_C03_GGTTGGAC

value: ICM


title: s1CP 1

value: 600ug/mL s1 calprotectin


title: s1CP3


title: subject1_white_rep2


title: WTCP 3

value: 300ug/mL WT calprotectin


title: subject2_beige_rep2


title: Hypothalamus, vehicle, rep6

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ-file generation and demultiplexing using bcl2fastq v. 2.20.0
STAR v2.7.2b was used to align sequence reads onto the GRCm38 mouse genome assembly, with the GENCODE version M25 gene model
reads were summarized onto genes by featureCounts v1.6.2 with the same gene model as when mapping, counting only fragments where both ends of the fragment were aligned
Assembly: mm10
Supplementary files format and content: featureCounts file containing gene-level mapped reads for the given sample

source_name: Hypothalamus

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen, US) according to the manufacturer’s protocol.
Libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan) as recommended by the manufacturer. Libraries were quantified with NuQuant, quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000.

value: Hypothalamus

value: vehicle


title: s1CP 2


title: embryo20_cell1

description: lane1_Ferdinand_Embryos_Plate6_A04_CAGATCTG


title: subject2_white_rep2

value: primary adipose stem cells

value: white adipogenic differentiation


title: WTCP 2


title: subject4_beige_rep2


title: 54950, mouse, hippocampus, 10Wk, control

value: hippocampus

value: male

value: wild type


title: Hypothalamus, GLP-1, rep5


title: Hypothalamus, conjugate 2, rep5

value: conjugate 2


title: embryo19_cell18

description: lane1_Ferdinand_Embryos_Plate6_H02_TAATCCCT

value: Blastocyst

value: WT

value: Male


title: embryo19_cell17

description: lane1_Ferdinand_Embryos_Plate6_H01_TAACAACT


title: Hypothalamus, conjugate 2, rep4


title: embryo20_cell5

description: lane1_Ferdinand_Embryos_Plate6_F03_CAGGGTCG

value: Female


title: subject3_beige_rep2

value: beige adipogenic differentiation


title: Vehicle 3

value: Newman

value: Bacterial cell

value: Vehicle


title: subject3_white_rep2


title: Vehicle 2


title: subject5_beige_rep1


title: Hypothalamus, vehicle, rep5


title: embryo19_cell16

description: lane1_Ferdinand_Embryos_Plate6_G02_AAGTGATA

value: ICM


title: embryo19_cell15

description: lane1_Ferdinand_Embryos_Plate6_G01_TTCTTAGC


title: Vehicle 1


title: embryo19_cell14

description: lane1_Ferdinand_Embryos_Plate6_F02_ACTTGGGG


title: Hypothalamus, vehicle, rep4

value: Hypothalamus


title: embryo19_cell13

description: lane1_Ferdinand_Embryos_Plate6_F01_CACCCGTC


title: subject6_beige_rep1


title: Hypothalamus, vehicle, rep3

value: vehicle


title: subject1_beige_rep1

value: primary adipose stem cells


title: embryo19_cell12

description: lane1_Ferdinand_Embryos_Plate6_E02_TATCTCCT


title: subject1_white_rep1

value: white adipogenic differentiation


title: Hypothalamus, vehicle, rep2


title: WTCP 1

value: 300ug/mL WT calprotectin


title: embryo19_cell11

description: lane1_Ferdinand_Embryos_Plate6_E01_GTAAGATA


title: subject2_beige_rep1


title: embryo19_cell10

description: lane1_Ferdinand_Embryos_Plate6_D02_AGGAGATT


title: Hypothalamus, GLP-1, rep4


title: subject2_white_rep1


title: embryo19_cell9

description: lane1_Ferdinand_Embryos_Plate6_D01_CAGGCTAA


title: Hypothalamus, GLP-1, rep3


title: subject4_beige_rep1


title: Hypothalamus, GLP-1/MK-801, rep6


title: embryo19_cell8

description: lane1_Ferdinand_Embryos_Plate6_C02_GTGCTACC


title: Hypothalamus, GLP-1/MK-801, rep5


title: subject3_beige_rep1


title: siSLFN12_DMSO_24h_rep3

city: Minoh

first: Kazuhide

last: Nakamura

state: Osaka

address: 5-1-35, Saito-aokita,

department: Department of Medical Innovations, Osaka Research Center for Drug Discovery

institute: Otsuka Pharmaceutical Co.,Ltd.

description: Gene expression in siSLFN12 PFSK1 cells treated with DMSO for 24 hours

hyb_protocol: After fragmentation, 1.65 ug of cRNA was hybridized to the Agilent expression microarray according to the manufacturer's protocols.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Data Processing Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

source_name: siSLFN12, DMSO, 24h, replicate3

label_protocol: Labeled cRNA was prepared from 1~5 ug of total RNA using Agilent's Quick Amp Labeling Kit.

growth_protocol: PFSK1 cells were cultured in in RPMI 1640 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin at 37˚C with 5% CO2.

extract_protocol: RNA was prepared using QIAshredder，RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN, NV) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer, and quality was monitored using the Agilent 2200 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with either non-targeted siRNA or SLFN12-targeted siRNA for 48 hours, followed by treatment with DMSO or OPB-171775 for 8 hours or 24 hours at 37ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: sirna


title: Hypothalamus, GLP-1, rep2

tag: treatment


title: siNTC_DMSO_24h_rep3

description: Gene expression in control PFSK1 cells treated with DMSO for 24 hours

source_name: siNTC (non-target control), DMSO, 24h, replicate3

value: Non-target


title: embryo19_cell7

description: lane1_Ferdinand_Embryos_Plate6_C01_GTAGAAGC

tag: developmental stage


title: siSLFN12_OPB_8h_rep3

description: Gene expression in siSLFN12 PFSK1 cells treated with OPB for 8 hours

source_name: siSLFN12, OPB, 8h, replicate3


title: subject3_white_rep1


title: embryo19_cell6

description: lane1_Ferdinand_Embryos_Plate6_B03_TACCGAGC


title: siNTC_OPB_24h_rep3

description: Gene expression in control PFSK1 cells treated with OPB for 24 hours

source_name: siNTC (non-target control), OPB, 24h, replicate3


title: siSLFN12_DMSO_8h_rep3

description: Gene expression in siSLFN12 PFSK1 cells treated with DMSO for 8 hours

source_name: siSLFN12, DMSO, 8h, replicate3


title: siSLFN12_OPB_24h_rep3

description: Gene expression in siSLFN12 PFSK1 cells treated with OPB for 24 hours

source_name: siSLFN12, OPB, 24h, relicatep3


title: Hypothalamus, conjugate 2, rep3


title: GANT61 treated hPASMCs 2

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: HG38
Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: patient pulmonary artherial

growth_protocol: Smooth Muscle cells Growth medium II (PromoCell)

extract_protocol:
Rneasy mini kit (QIAGEN)
Illumina Stranded mRNA Prep

treatment_protocol: Gant61 20uM in Smooth muscle cells growth medium II

value: patient pulmonary artherial

value: Smooth muscle cells

value: GANT61 20 uM 24h


title: subject5_white_rep1


title: embryo19_cell5

description: lane1_Ferdinand_Embryos_Plate6_B02_TTACTCGC

source_name: Blastocyst

value: Blastocyst

value: WT


title: siNTC_OPB_8h_rep3

description: Gene expression in control PFSK1 cells treated with OPB for 8 hours

source_name: siNTC (non-target control), OPB, 8h, replicate3


title: siNTC_DMSO_8h_rep3

description: Gene expression in control PFSK1 cells treated with DMSO for 8 hours

source_name: siNTC (non-target control), DMSO, 8h, replicate3


title: embryo19_cell4

description: lane1_Ferdinand_Embryos_Plate6_B01_TGTCTATC

value: Male


title: Hypothalamus, GLP-1/MK-801, rep4


title: GANT61 treated hPASMCs 1


title: embryo19_cell3

description: lane1_Ferdinand_Embryos_Plate6_A03_ACAGTGGT


title: Hypothalamus, conjugate 2, rep2

value: conjugate 2


title: Control hPASMCs 1

value: vehicle ethanol


title: Hypothalamus, GLP-1, rep1


title: Hypothalamus, conjugate 2, rep1


title: Hypothalamus, vehicle, rep1


title: Control hPASMCs 2


title: Hypothalamus, GLP-1/MK-801, rep3


title: embryo19_cell1

description: lane1_Ferdinand_Embryos_Plate6_A01_ATCACGTT


title: siSLFN12_DMSO_24h_rep2

source_name: siSLFN12, DMSO, 24h, replicate2


title: Hypothalamus, GLP-1/MK-801, rep2


title: embryo18_cell3

value: Female


title: siNTC_OPB_24h_rep2

source_name: siNTC (non-target control), OPB, 24h, replicate2


title: Hypothalamus, GLP-1/MK-801, rep1


title: siNTC_DMSO_24h_rep2

source_name: siNTC (non-target control), DMSO, 24h, replicate2


title: embryo18_cell2


title: Accumbens, GLP-1/MK-801, rep8

data_processing:
FASTQ-file generation and demultiplexing using bcl-convert v. 4.0.3
Align to genome and determine transcript and gene counts with the nfcore-rnaseq pipeline v. 3.10.1 using the STAR->Salmon workflow.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated file containing the raw gene counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample
Supplementary files format and content: Tab-seperated file containing the raw transcript counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample

source_name: Accumbens

value: Accumbens


title: siSLFN12_OPB_24h_rep2

source_name: siSLFN12, OPB, 24h, replicate2


title: siSLFN12_OPB_8h_rep2

source_name: siSLFN12, OPB, 8h, replicate2


title: Accumbens, GLP-1/MK-801, rep7


title: embryo19_cell2

description: lane1_Ferdinand_Embryos_Plate6_A02_TTAGGCAT

data_processing:
Raw reads were processed as previously (https://doi.org/10.1038/s41467-018-03149-4), aligning to the GRCh38 reference genome using Hisat2 (https://doi.org/10.1038/s41587-019-0201-4).
Gene expression counts were computed from the mapped data using the featureCounts function within RSubread (https://doi.org/10.1093/nar/gkz114).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

value: ICM


title: embryo18_cell4


title: siNTC_DMSO_8h_rep2

source_name: siNTC (non-target control), DMSO, 8h, replicate2


title: siNTC_OPB_8h_rep2

source_name: siNTC (non-target control), OPB, 8h, replicate2


title: siSLFN12_OPB_24h_rep1

source_name: siSLFN12, OPB, 24h, replicate1


title: siSLFN12_DMSO_24h_rep1

source_name: siSLFN12, DMSO, 24h, replicate1


title: embryo17_cell1


title: embryo16_cell12


title: Accumbens, GLP-1/MK-801, rep5


title: Accumbens, GLP-1/MK-801, rep2


title: Accumbens, GLP-1/MK-801, rep6


title: embryo17_cell2


title: embryo16_cell10


title: Accumbens, GLP-1/MK-801, rep3


title: embryo16_cell9


title: embryo16_cell8


title: embryo18_cell1


title: Accumbens, GLP-1, rep8


title: embryo16_cell7


title: Hypothalamus, GLP-1, rep6

source_name: Hypothalamus

value: Hypothalamus


title: siSLFN12_DMSO_8h_rep2

source_name: siSLFN12, DMSO, 8h, replicate2


title: Chondrocyte_trunk_biolRep3

city: Muenster

first: Kleio

last: Petratou-Busswinkel

address: Röntgenstraße 16

institute: Institute for Cardiovascular Organogenesis and Regeneration

description: GFP negative, mCherry positive cells

data_processing:
QC of sequences, adapter trimming and duplicate removal using fastp package (with --dedup option)
Sequence alignment to genome using the STAR aligner
samtools to sort and index aligned reads
reads counted using the featureCounts command from the Subread package
Assembly: danRer11
Supplementary files format and content: tab-deliminated text files including raw count for each sample (7th column)

organism: Danio rerio

source_name: trunk

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN, 74034).
Samples were sent to Eurofins Genomics for library preparation and paired-end sequencing with the INVIEW Transcriptome Ultra Low service (2x 150). Per sample, 15M reads were sequenced.

value: trunk

value: trunk chondrocyte

tag: Stage

value: 15 days post fertilisation


title: siNTC_DMSO_24h_rep1

source_name: siNTC (non-target control), DMSO, 24h, replicate1


title: Accumbens, GLP-1, rep7


title: siNTC_OPB_8h_rep1

source_name: siNTC (non-target control), OPB, 8h, replicate1


title: siSLFN12_DMSO_8h_rep1

source_name: siSLFN12, DMSO, 8h, replicate1


title: Chondrocyte_trunk_biolRep2

description: GFP negative, mCherry positive cells


title: embryo16_cell6

source_name: Blastocyst

extract_protocol:
Cells were collected directly into 2.5 μl methyltransferase reaction mixture which was comprised of 1 × M.CviPI Reaction buffer, 2 U M.CviPI, 160 μM S-adenosylmethionine, 1 U μl−1 RNAsein, 0.1% IGEPAL then incubated for 15 min at 37 °C. The reaction was stopped and the RNA preserved with the addition of 5 μl RLT plus.
Single-cell RNA sequencing libraries were prepared according to the RNA half of the scNMT-seq protocol (https://doi.org/10.1038/s41467-018-03149-4). Briefly, biotinylated oligo-dT was bound to magnetic beads which were added to single-cell lysates in 96w plates. The captured mRNA was then reverse transcribed and PCR amplified on beads accordingto the Smartseq2 protocol (https://doi.org/10.1038/nprot.2016.138,https://doi.org/10.1038/nprot.2014.006). Indexed Illumina libraries were prepared from the amplified cDNA using Nextera XT reagents and then pooled and sequenced on a HiSeq 2000 instrument using 75bp paired-end reads.


title: siNTC_OPB_24h_rep1

source_name: siNTC (non-target control), OPB, 24h, replicate1


title: siNTC_DMSO_8h_rep1

source_name: siNTC (non-target control), DMSO, 8h, replicate1


title: Accumbens, GLP-1/MK-801, rep4


title: embryo16_cell11


title: Chondrocyte_trunk_biolRep1

description: GFP negative, mCherry positive cells


title: Chondrocyte_head_biolRep3

description: GFP negative, mCherry positive cells

source_name: head

value: head

value: head chondrocyte


title: embryo16_cell5


title: Accumbens, GLP-1, rep5

source_name: Accumbens


title: embryo16_cell4


title: Chondrocyte_head_biolRep2

description: GFP negative, mCherry positive cells


title: Accumbens, GLP-1, rep4


title: Accumbens, GLP-1/MK-801, rep1


title: HDPCs, MDL, osteogenic differentiation, bio rep3

city: Chengdu

first: XUEYANG

last: LIAO

state: Sichuan

address: NO.14 3rd section of Renminnan Road

institute: Sichuan university

data_processing:
Clustering and sequencing: After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Quality control: The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: tab-delimited xls files include RPKM values for each Sample

source_name: human dental pulp

growth_protocol: Freshly extracted third molars from patients aged 18-22 years were collected at West China Hospital of Stomatology, Sichuan University were collected. The pulp was removed from the teeth, and the tissue was cut into small pieces. And they were digested by 3 mg/mL collagenase type I in a 37°C water bath for 45 min. Then the supernatant was discarded before centrifuging at 1500rpm for 5min. The digested cells were then transfered to a 10cm cell culture dish and incubate in a CO2 incubator with growth medium (10% FBS+1% Penicillin/Streptomycin in DMEM). The medium was changed every 2-3 days. Dental pulp cells of the 3rd-5th generation are used for this study. For osteogenic differentiation, the mineralization induction solution (Growth medium, 4 mM sodium β-glycerophosphate, 10-6 mol/L dexamethasone, 50 μg/mL L-ascorbic acid) was added when the cells reached 70% confluence.

extract_protocol:
Total RNA was collected by tryzol from HDPCs with indicated treatment. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Treatment for normal condition HDPCs: HDPCs pre-treated with DMSO or MDL-800 for 2hrs then changed to complete medium. Cells were cultured for 24hrs before harvest. Osteogenic differentiation treatment for HDPCs:  DMSO or MDL-800 pre-treated for 2hrs then changed to osteogenic medium for every medium change. Osteogenic differentiation with this medium change method every other day for 7 days before harvest.

value: human dental pulp

value: primary cells of human dental pulp cells

value: Osteogenic differentiated for 7days with MDL-800 pre-treatment.


title: embryo16_cell3

value: Blastocyst


title: HDPCs, MDL, osteogenic differentiation, bio rep2

value: WT


title: Chondrocyte_head_biolRep1

description: GFP negative, mCherry positive cells


title: HDPCs, MDL, osteogenic differentiation, bio rep1


title: Accumbens, GLP-1, rep3


title: HDPCs, DMSO, osteogenic differentiation, bio rep3

value: Osteogenic differentiated for 7days with DMSO pre-treatment.


title: Osteoblast_trunk_biolRep3

description: GFP positive, mCherry negative cells

value: osteoblast (non-classical)


title: Accumbens, GLP-1, rep1


title: embryo16_cell1


title: Osteoblast_trunk_biolRep2

description: GFP positive, mCherry negative cells


title: HDPCs, DMSO, osteogenic differentiation, bio rep2


title: Accumbens, GLP-1, rep2


title: HDPCs, DMSO, osteogenic differentiation, bio rep1


title: embryo15_cell16


title: embryo15_cell17


title: Osteoblast_head_biolRep3

description: GFP positive, mCherry negative cells

value: osteoblast (classical)


title: Accumbens, MK-801, rep8


title: Accumbens, MK-801, rep6


title: HDPCs, MDL, complete medium, bio rep3

value: MDL-800 pre-treated for 2hrs and harvested at 24hrs


title: embryo15_cell15

value: Female


title: Accumbens, MK-801, rep7

value: Accumbens


title: Osteoblast_head_biolRep2

description: GFP positive, mCherry negative cells


title: HDPCs, MDL, complete medium, bio rep2


title: Osteoblast_head_biolRep1

description: GFP positive, mCherry negative cells


title: Accumbens, MK-801, rep5


title: embryo15_cell14

value: ICM


title: embryo16_cell2


title: HDPCs, MDL, complete medium, bio rep1


title: Accumbens, MK-801, rep4


title: Accumbens, GLP-1, rep6


title: T1-Tax-3

city: İstanbul

first: Tugba

last: Bagci-Onder

address: Rumelifeneri Yolu, Sarıyer

department: Koç University Research Center for Translational Medicine

country: Turkey

institute: Koç University

description:
SUM159-T1-160_TAX123vsAP123_nt.sgrna_summary.txt
SUM159-T1-160_TAX123vsDMSO123_nt.sgrna_summary.txt
T1-TaxvsAP_gene_summary.txt
T1-TaxvsDMSO_gene_summary.txt

data_processing:
NGS was performed at Genewiz (NJ, USA) by using Hiseq (Illumina) with at least 10 million reads/sample. Sequencing reads from R1 fastq files were aligned to sgRNA library and counted using MAGeCK (v0.5.8). Biological replicates were presented as individual input files for counting and results were normalized as Read Per Million (RPM) and converted to Log2 values. Counts of sgRNAs were then combined with median normalization to obtain gene level log2 fold changes. p<0.05 cutoff was applied to gene level analysis to identify significantly depleted genes.
Assembly: For anaylsis of CRISPR screens, sgRNAs were counted by matching to custom CRISPR Screen library; Epigenetic Knock-out Library (EPIKOL).
Supplementary files format and content: sgRNA_summary files contain counts, logfoldchanges, p values and FDRs for triplicate samples of the indicated groups for each sgRNA
Supplementary files format and content: gene_summary files contain negative depletion rank, logfoldchange, p value for each gene (total effects of 10 sgRNAs per gene)
Library strategy: CRISPR Amplicon sequencing

growth_protocol: SUM159PT cells were cultured in Ham’s F12 nutrient mix (Gibco, USA) supplemented with 5% FBS, 5 μg/ml insulin (Sigma-Aldrich, USA), 1 μg/ml hydrocortisone (Sigma-Aldrich, USA) and 10 mM HEPES (Thermo Fisher, USA). Cells were maintained in a humidified incubator at 37oC with 5% CO2 level.

extract_protocol:
Genomic DNA was isolated using Nucleospin Tissue kit (Macherey-Nagel, Germany) according to manufacturer’s instructions.
Next generation sequencing (NGS) libraries were prepared as described. Briefly, in the first PCR, 13.2 μg of gDNA was used as a template to achieve 250x coverage of the sgRNA library. In the second round, NGS (Illumina) adapters (stagger, index and index read primer sequences) were added at the ends of PCR amplicons. Products were run on 2% agarose gel, purified by using MN Nucleospin Gel and PCR Cleanup kit. NGS was performed at Genewiz (NJ, USA) by using Hiseq (Illumina) with at least 10 million reads/sample.

treatment_protocol: Epigenetic Knockout Library (EPIKOL) that targets 779 genes including several controls was used and viruses were generated as described. After Cas9-expressing T1-160 cells were generated, pooled lentiviral EPIKOL was transduced as 1000x representation with MOI 0.4. Transduced cells were selected with 5 μg/ml puromycin in the presence of 20 μM verapamil for 4 days and 8 million cells were collected as initial timepoint. Cells were divided into two groups and treated with either DMSO as vehicle or 160 nM Taxol until they reach 16 population doublings. At the end of culturing period, final cell pellets were collected as 8 million.

value: Taxol-resistant Invasive Breast Carcinoma

value: Chromatin focused CRISPR/Cas9 library infection - Taxol (160 nM)

value: After 16 population doublings

tag: collection

value: Last collection. Epikol-infected cells were divided into 2 groups after puromycin selection. This group was treated with 160 nM Taxol and pellets were collected after 16 population doublings.


title: embryo15_cell13

city: Edinburgh

first: Lawrence

last: Bates

address: Crewe Road

institute: University of Edinburgh


title: embryo15_cell12


title: Accumbens, MK-801, rep3


title: T1-Tax-2

description:
Tax samples were compared to DMSO group to reveal any genes regulating Taxol resistance and causing cell death upon loss in the presence of Taxol.
SUM159-T1-160_TAX123vsAP123_nt.sgrna_summary.txt
SUM159-T1-160_TAX123vsDMSO123_nt.sgrna_summary.txt
T1-TaxvsAP_gene_summary.txt
T1-TaxvsDMSO_gene_summary.txt


title: Accumbens, MK-801, rep2


title: Osteoblast_trunk_biolRep1

description: GFP positive, mCherry negative cells

value: trunk

value: 15 days post fertilisation


title: T1-Tax-1

description:
Tax samples were compared to AP group to reveal any genes essential for cell survival of the Taxol resistant cells.
SUM159-T1-160_TAX123vsAP123_nt.sgrna_summary.txt
SUM159-T1-160_TAX123vsDMSO123_nt.sgrna_summary.txt
T1-TaxvsAP_gene_summary.txt
T1-TaxvsDMSO_gene_summary.txt


title: HDPCs, DMSO, complete medium, bio rep2

value: human dental pulp

value: primary cells of human dental pulp cells

value: DMSO pre-treated for 2hrs and harvested at 24hrs


title: HDPCs, DMSO, complete medium, bio rep1

value: WT


title: embryo15_cell10

value: Blastocyst


title: T1-DMSO-3

description:
SUM159-T1-160_DMSO123vsAP123_nt.sgrna_summary.txt
T1-DMSOvsAP_gene_summary.txt

value: Chromatin focused CRISPR/Cas9 library infection - DMSO

value: Last collection. Epikol-infected cells were divided into 2 groups after puromycin selection. This group was treated with DMSO and pellets were collected after 16 population doublings.


title: NCO-3(NCO_rep3)

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: CD36 knockdown

value: decitabine


title: Accumbens, MK-801, rep1

value: Accumbens


title: Accumbens, Vehicle, rep8

value: Vehicle


title: NCO-2(NCO_rep2)


title: embryo15_cell8

value: ICM

value: Female


title: Accumbens, Vehicle, rep7


title: T1-DMSO-2

value: Taxol-resistant Invasive Breast Carcinoma

value: After 16 population doublings


title: embryo15_cell7


title: T1-DMSO-1


title: embryo15_cell9


title: NCO-1(NCO_rep1)


title: Accumbens, Vehicle, rep6


title: NC1-3(NC1_rep3)


title: HDPCs, DMSO, complete medium, bio rep3


title: embryo15_cell6


title: T1-AP-3

description: SUM159-T1-160_DMSO123vsAP123_nt.sgrna_summary.txt

value: Chromatin focused CRISPR/Cas9 library infection - no drug

value: After puromycin selection

value: Initial collection (reference point). EPIKOL-transduced T1-160 cells were collected right after puromycin selection.


title: NC1-2(NC1_rep2)


title: embryo15_cell5


title: embryo15_cell11


title: siSLFN12_OPB_8h_rep1

description: Gene expression in siSLFN12 PFSK1 cells treated with OPB for 8 hours

source_name: siSLFN12, OPB, 8h, replicate1


title: T1-AP-1

description:
Counts of after puromycin (AP) samples can be seen in DMSOvsAP or TAXvsAP comparison sheets.
SUM159-T1-160_DMSO123vsAP123_nt.sgrna_summary.txt


title: Accumbens, Vehicle, rep4


title: embryo15_cell4


title: Accumbens, Vehicle, rep3


title: HDPC, anti-H3K56ac, abcam, bio rep2 K56acD_2

description: HDPC, anti-H3K56ac, abcam, bio rep2

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Frist at all, we use FastQC performs basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below: (1) Remove low-quality reads: The reads that mean quality value less than 20 were removed. (2) Remove the reads that contain more than 15 percent N bases. (3) Remove adapters. Remove the reads that alignment with the adapter sequence. (4) Drop reads blow the 18 bases long after trimming. (5) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last,we use FastQC performs basic statistics on the quality of the clean reads.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
Fragmentsizeestimation: For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS), Genome Biol). MACS scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
Strand Cross Correlation: Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on forward and reverse strands centered around the binding site. get.binding.characteristics function of SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
Peakdetection: After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed
Peakannotation: The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. PeakAnnotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Besides, the distribution of peak summits on different function regions, such as 5’ UTR, CDS, 3’UTR, was performed.  Peak related genes can be confirmed by PeakAnnotator, and then Gene Ontology (GO) enrichment analysis of performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by peak related genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
Differentpeakanalysis: Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Freshly extracted third molars from patients aged 18-22 years were collected at West China Hospital of Stomatology, Sichuan University were collected. The pulp was removed from the teeth, and the tissue was cut into small pieces. And they were digested by 3 mg/mL collagenase type I in a 37°C water bath for 45 min. Then the supernatant was discarded before centrifuging at 1500rpm for 5min. The digested cells were then transfered to a 10cm cell culture dish and incubate in a CO2 incubator with growth medium (10% FBS+1% Penicillin/Streptomycin in DMEM). The medium was changed every 2-3 days. Dental pulp cells of the 3rd-5th generation are used for this study.

extract_protocol:
HDPCs were fixed with 1% formaldehyde for 1min at room temperature to crosslink chromatin. 125mM glycine was added to the plates to stop crosslinking. Cells were then washed then lysed with lysis buffer supplemented with phosphatase and protease inhibitor cocktails. Purified nuclei were collected by centrifuge and then incubated with nuclease to get mononucleosomes. Soluble chromatin was then subjected to immunoprecipitation as described in manufacture’s protocol(MM_NF-17-375, Millipore).
1.DNA quantification and qualification: ChIP DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0Flurometer(LifeTechnologies,CA,USA); 2.Library preparation and quantification: The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Library quality was assessed on the Agilent Bioanalyzer 2100 system. Briefly, In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HDPCs pre-treated with DMSO or MDL-800 for 2hrs then changed to complete medium. Cells were cultured for 24hrs before harvest.

value: human dental pulp

value: H3K56ac, 5ug, abcam, ab195478

value: primary cells of human dental pulp cells

value: DMSO pre-treated for 2hrs, complete medium cultured for 24hrs before harvest


title: HDPC, anti-H3K56ac, abcam, bio rep1 K56acD_1

description: HDPC, anti-H3K56ac, abcam, bio rep1

value: WT


title: NC1-1(NC1_rep1)

value: cell line


title: KO1-3(KO1_rep3)


title: Accumbens, Vehicle, rep2


title: KO1-2(KO1_rep2)


title: HDPC, anti-H3K56ac, abcam, bio rep2 K56ac8_2

description: HDPC, anti-H3K56ac, abcam, bio rep2

value: MDL-800 pre-treated for 2hrs, complete medium cultured for 24hrs before harvest


title: Accumbens, Vehicle, rep1


title: HDPC, anti-H3K56ac, abcam, bio rep1 K56ac8_1

description: HDPC, anti-H3K56ac, abcam, bio rep1


title: embryo15_cell2

value: Blastocyst


title: KO1-1(KO1_rep1)


title: embryo15_cell1


title: embryo14_cell10

value: Male


title: HDPC, anti-H3K9ac, abcam, bio rep2 K9acD_2

description: HDPC, anti-H3K9ac, abcam, bio rep2

value: H3K9ac, 5ug, abcam, ab4441


title: Brain stem, GLP-1/MK-801, rep7

source_name: Brain stem

value: Brain stem


title: embryo14_cell9

value: ICM


title: Accumbens, Vehicle, rep5

value: Accumbens

value: Vehicle


title: HDPC, anti-H3K9ac, abcam, bio rep1 K9acD_1

description: HDPC, anti-H3K9ac, abcam, bio rep1


title: MV4-11, KO, rep4

description: KO4 (MV4-11, KO, rep4)

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Allgene_info.xlsx reports counts and FPKMs for all samples

growth_protocol: MV4-11 cells were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

treatment_protocol: CRISPR-Cas9-based CD36 knockout in MV4-11 cells

value: human acute myeloid leukemia cells

value: CD36 knockout


title: Brain stem, GLP-1/MK-801, rep6


title: MV4-11, KO, rep2

description: KO2 (MV4-11, KO, rep2)


title: HDPC, anti-H3K9ac, abcam, bio rep2 K9ac8_2

description: HDPC, anti-H3K9ac, abcam, bio rep2


title: HDPC, anti-H3K9ac, abcam, bio rep1 K9ac8_1

description: HDPC, anti-H3K9ac, abcam, bio rep1


title: MV4-11, KO, rep1

description: KO1 (MV4-11, KO, rep1)


title: Brain stem, GLP-1/MK-801, rep5


title: embryo14_cell7


title: Brain stem, GLP-1/MK-801, rep4


title: HDPCs, cross-linked and sonicated only Input

description: HDPCs, cross-linked and sonicated only

value: complete medium cultured


title: embryo14_cell6


title: embryo15_cell3

value: Female


title: Brain stem, GLP-1/MK-801, rep8


title: MV4-11, NC, rep4

description: NC4 (MV4-11, NC, rep4)

value: control


title: MV4-11, NC, rep3

description: NC3 (MV4-11, NC, rep3)


title: HDPCs, IgG, Millipore

description: HDPCs, IgG, Millipore

value: human dental pulp

value: normal rabbit IgG, 5ug, Millipore

value: primary cells of human dental pulp cells


title: embryo14_cell5

value: WT


title: TAC_treated_human_iPSC_derived_neurons_rep3

city: Houston

first: Hong Seok

last: Shim

state: TX

institute: MD Anderson Cancer Center

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling. bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files. Fastq files were aligned to the human reference genome (GRCh38) using HISAT2 software and assembled using StringTie. R package DESeq2 was used for data normalization and differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: TAC-treated human iPSC-derived neurons

growth_protocol: Differentiated neurons were cultured in neural differentiation media (DMEM/F12, 1x GlutaMax, 1x N2, 1x B27 (Invitrogen), 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 µM dibutyryl-cyclic AMP, and 0.2 µM ascorbic acid (Sigma).

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Human iPSCs were treated with DMSO or TAC.

value: human iPSC-derived neurons

value: TAC-treated


title: Brain stem, GLP-1/MK-801, rep2


title: MV4-11, KO, rep3

description: KO3 (MV4-11, KO, rep3)


title: Brain stem, GLP-1/MK-801, rep1


title: TAC_treated_human_iPSC_derived_neurons_rep2


title: TAC_treated_human_iPSC_derived_neurons_rep1


title: embryo14_cell3

value: Blastocyst

value: Male


title: Brain stem, GLP-1, rep8

value: Brain stem


title: MV4-11, NC, rep1

description: NC1 (MV4-11, NC, rep1)


title: embryo14_cell8

value: ICM


title: Brain stem, GLP-1, rep7


title: red1∆ cells, rep_2

city: Shanghai

first: Tomoyasu

last: Sugiyama

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

data_processing:
The raw data was checked by FastQC v0.11.6
Clean reads were aligned to the Schizosaccharomyces japonicus genome using STAR (2.5.3a)
The expression of the transcript was calculated by FPKM using StringTie v1.3.1c
Assembly: S. japonicus genome sequencing data; https://www.japonicusdb.org/status/genome-overview
Supplementary files format and content: an excel file containing RPKM values for each gene (a total of 7001 annotated transcripts) in each sample

organism: Schizosaccharomyces pombe

source_name: whole cell

growth_protocol: All the S. pombe cells were grown in YES media (0.5% yeast extract, 3% glucose, and 75 mg/L of adenine, histidine, leucine, and uracil) at 32°C

extract_protocol:
Extracted total RNAs using MasterPure™ Yeast RNA Purification Kit (Lucigen)
NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760)

value: whole cell

value: red1 mutation


title: DMSO_treated_human_iPSC_derived_neurons_rep3

source_name: DMSO-treated human iPSC-derived neurons

value: DMSO-treated


title: embryo14_cell1


title: Brain stem, GLP-1, rep6


title: mug174∆ cells, rep_2

value: mug174 deletion


title: Brain stem, GLP-1/MK-801, rep3


title: Brain stem, GLP-1, rep5


title: embryo13_cell37

description: lane1_Ferdinand_Embryos_Plate1_H04_GTTATGGC


title: embryo14_cell4


title: MV4-11, NC, rep2

description: NC2 (MV4-11, NC, rep2)

value: human acute myeloid leukemia cells


title: embryo13_cell36

description: lane1_Ferdinand_Embryos_Plate1_H03_AAACATCA

value: Female


title: DMSO_treated_human_iPSC_derived_neurons_rep1


title: embryo13_cell35

description: lane1_Ferdinand_Embryos_Plate1_H02_AGGACACT


title: TAC-treated_MRC5_rep3

source_name: TAC-treated human MRC5 cells

growth_protocol: Fibroblasts were cultured in EMEM with 10% Fetal Bovine Serum (FBS), 1X penicillin/streptomycin (Invitrogen).

treatment_protocol: Fibroblasts were treated with DMSO or TAC.

value: human MRC5 cells


title: mug174∆ cells, rep_1


title: Brain stem, GLP-1, rep3


title: embryo14_cell2


title: Wild-type cells, rep_1


title: Brain stem, GLP-1, rep4


title: TraPR small RNA-seq: ago18HT-5mm-rep3

city: Wuhan

first: Junpeng

last: Zhan

address: 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
library strategy: TraPR (Trans-kingdom, rapid, affordable Purification of RNA-induced silencing complexes (RISCs)) small RNA-seq
To quantify phasiRNA abundance, sRNA-seq reads were mapped to the respective Zea genomes using Bowtie v1.3.1.Reads mapped to PHAS loci were counted using featureCounts v1.6.3 and normalized to counts per million (CPM) using edgeR v4.0.2. Differential expression analyses were performed using edgeR with a generalized linear model-based method.
Assembly: B73 RefGen_v5
Supplementary files format and content: CPM tables

organism: Zea mays subsp. mays

source_name: anther

extract_protocol:
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TraPR Small RNA Isolation kit (Lexogen)
sRNA-seq libraries were prepared using a Somagenics RealSeq-AC miRNA library kit following the manufacturer’s protocol.

value: anther

value: mostly B73

tag: group

tag: molecule subtype

value: Small RNA - Argonaute loaded


title: TAC-treated_MRC5_rep2

value: WT


title: TAC-treated_MRC5_rep1


title: Wild-type cells, rep_2


title: red1∆ cells, rep_1


title: TraPR small RNA-seq: ago18HT-5mm-rep2


title: DMSO_treated_human_iPSC_derived_neurons_rep2

value: human iPSC-derived neurons


title: DMSO-treated_MRC5_rep3

source_name: DMSO-treated human MRC5 cells


title: embryo13_cell33

description: lane1_Ferdinand_Embryos_Plate1_G04_AGGTATCC


title: embryo13_cell32

description: lane1_Ferdinand_Embryos_Plate1_G03_AGCCGTGA


title: Brain stem, GLP-1, rep1


title: Brain stem, GLP-1, rep2


title: TraPR small RNA-seq: ago18HT-5mm-rep1


title: DMSO-treated_MRC5_rep2


title: embryo13_cell31

description: lane1_Ferdinand_Embryos_Plate1_G02_TCGATGCG


title: Brain stem, MK-801, rep8


title: Brain stem, MK-801, rep7


title: TraPR small RNA-seq: ago18HT-2mm-rep3


title: embryo13_cell30

description: lane1_Ferdinand_Embryos_Plate1_G01_TGAGTAAG